I meant that for me it is a bug that block the perk so maybe there could be a way to fix it.

Typically it occured after I selected the perk, after I went to space and accept an escort mission (I fought with pirate in free fight but nothing happened). But then, as the other help window, it doesn't appears anymore.
So maybe there is a boolean function associated to each popup window that switchs when a specific action launched the popup.

As I was unable to save I cannot say if it would have work after, and the fact I cannot have back the popup even after using an old save means that there is a bug somewhere. And as it is a popu window that is associated to a perk I believe that the bug is somewhere in a logical condition between, the perk, the popup window and the script that initiate the popup.

Maybe I am completely wrong but as it worked once I am sure that is programmed in the game but need to be fix.